Tag Archives: ecology

Raman spectroscopy is awesome and you should too

Sir_CV_Raman
Sir C.V. Raman, the namesake of Raman spectroscopy. Image from Wikipedia.

Raman spectroscopy is awesome. But these days it is rapidly getting more awesome. Here are a just a few new reasons to love Raman spectroscopy:

  1. It measures the metabolism of single living bacterial cells (in conjunction with stable isotopes).
  2. In mere seconds, it quantifies essentially all the various gases in 27 nanoliters of human breath.
  3. It does video-speed label-free chemical imaging on microscopic scales.
  4. It tracks in real-time the yields and titers of chemical and bichemical reactions, even at small scales.

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Open seminars: a new and good idea

One of the things I liked best about being an academic researcher was group meeting. Every week, a different student or scholar would present some fresh data from their own projects. And these meetings were casual and interactive: you could interrupt any time with questions.

In industry chances to keep up with fundamental discovery science outside of your own core area can be more limited. Folks (mainly job candidates) do visit the corporate world to give research talks, and of course industrial scientists still attend conferences, but those interactions — while invaluable — aren’t as informal. The work presented is always well-polished, and people usually shy away from long technical questions and discussion.

That isn’t the case with MicroSeminar: it’s a new(ish) online-only, publicly accessible research seminar in microbiology created by Jennifer Biddle and Cameron Trash. Once a month or so, people from all over the world log into a Google Plus hangout, or watch YouTube — live or when you get free time — as some of the new fresh hot research in environmental microbiology, microbial ecology, and biogeochemistry gets presented. The feel is informal, with lots of Q&A, and you don’t even have to leave home (or bed!). Here are some of the talks I’ve enjoyed so far.

And don’t just take my word for it. Here are some similar thoughts from Pat Schloss:

The cost of going to ISME [a conference] in Korea this summer? In the thousands. Cost of sitting with your laptop watching a seminar? Zilch. Jennifer is correct that this won’t kill conferences. Conferences have a huge social aspect and provide great opportunities for networking. But the science is frequently stale and pulled from the pages of last year’s AEM [a journal]. I think there’s great potential with this model to change how we disseminate information to our colleagues. Like I said, I think this is big, deserving of your attention and perhaps others will create parallel online seminar series that are either more specialized or more general.

And if microbiology isn’t your cup of tea? If you’re an academic in a different field? Like Pat says, maybe you should start another online seminar program like this one.

Where do all those raindrops go?

An earlier Fact of the Day noted that about 15,000 km3 of rain falls on the North American continent every year. Where do all those raindrops go? One approach to measuring and tracking water flows is “water footprint” analysis. This approach to the question would seem on a cursory examination to indicate that more than one in every twenty-five raindrops in all of North America goes to producing beef, chicken, soybeans, wheat, and corn in the United States. Here’s a table of some water footprints for various agricultural products multiplied by annual US production.

Water Footprints of agricultural products and production volume in the U.S. Note: Don't believe these numbers!

Water Footprints of agricultural products and production volume in the U.S.


Does that number seem high? It does to me. In fact I don’t believe them at all! The main problem is in the way the water footprint analysis is done. Some of the problems I have with water footprint analysis I have discussed before, at least in the abstract. I’d like to offer more specific examples of what I find misleading about the water footprint.

1. Inconsistent time frame of analysis. The water footprint for beef, as calculated, stems mainly from the water inputs into feed production over the entire lifespan of the animal, from birth to slaughter. Waterfootprint.org assumes cattle take three years to reach maturity, which sounds reasonable enough. Certainly it takes water to grow feed for the cattle in all three years of its life. But the failure to base the water footprint of a product on some consistent unit of time leads to some strange consquences. Take a calf named Betsy. Some of the same water molecules that grows the grass that feeds Betsy in the year after her birth get evapotranspirated back into the atmosphere; others get diverted to streams and rivers and flow to the ocean, from where the evaporate again. Eventually they fall again as rain. The turnover time for this process is much less than a year. For example, water draining to the Mississippi River basin reaches the Gulf of Mexico in less than one month. The mean residence time of moisture in soil before evaporation might be ~90 days. (These numbers are coming from Figures 5.5 and 9.1 of this book.) Thus, those water molecules that we counted as part of the year I water footprint for production of our hypothetical calf might be the same molecules that are counted again in year 2!

COUNTERPOINT AND RESPONSE: Prof. A. Y. Hoekstra, perhaps the chief proponent of water footprint analysis, points to FAQ Question 4 at the waterfootprint.org site:

…But in a certain period one cannot use more water than is available. A river can be emptied and in the long term one cannot take more water from lakes and groundwater reservoirs than the rate with which they are recharged. The water footprint measures the amount of water available in a certain period that is consumed (i.e. evaporated) or polluted. In this way, it provides a measure of the amount of available water appropriated by humans. The remainder is left for nature.

To me, this “answer” acknowledges the problem but provides no indication that water footprint analysis solves it.  Water footprint analysis does not reveal the “amount of available water” that humans could appropriate “in a certain period”, it reveals the amount of water that humans do appropriate in a certain period.  And it appears that in many cases, the period used for water footprint analysis is longer than the time it takes the water cycle to recharge itself.

2. Failure to consider substitution effects. At waterfootprint.org, note the following text:

… to produce one kilogram of boneless beef, we use about 6.5 kg of grain, 36 kg of roughages, and 155 litres of water (only for drinking and servicing). Producing the volume of feed requires about 15300 litres of water in average.

In the US, the grain is probably mostly corn. Even if it were the ostensibly more water-intensive wheat, the water footprint per kg of beef from grain would be only 8450 L (from 6.5 kg grain per kg of beef × 1300 L of water per kg of wheat). That’s only about half of the feed water. The remainder, 7100 L, must come from the roughage. At waterfootprint.org, roughage is described as “pasture, dry hay, silage and other roughages”. Fair enough. But what happens if the beef industry decides it doesn’t need to produce Betsy, and as a result, Betsy is never born? Do we save 7100 L of water for every kg that Betsy would have weighed in year 3 of her life? Possibly, but only if none of the pasture, dry hay, and silage that would have gone to feed Betsy is produced in her absence. If Betsy’s portion of hay is grown anyway, it will still evapotranspirate water that could have been directed to other uses, even if the hay is left on the field instead of harvested. In short, it seems far easier to change the water footprint attributed to a product than it does to change the perturbations to the water cycle caused by the production of that product.

COUNTERPOINT AND RESPONSE: Prof. Hoekstra says: “If not appropriated for human consumption (e,g, hay as input of cows that provide meat), then the water is available to sustain natural vegetation (or in the case of river water: sustain aquatic life)”.  True enough…but why design a method of water use accounting that stacks the deck in favor of “natural” vegetation so highly?  From a water use perspective, what is the difference between a prairie grazed by a “natural” bison population which people do not eat, and a pasture grazed by cattle, which people do eat, other than in the former case people have less food?

3. Double-counting. Even if Betsy does get produced, and even if we ignore the incommensurate time scales of Betsy’s life and the terrestrial water cycle, there’s yet another problem in adding up the water footprints of various agricultural commodities, as I did above. In the US, about 55% of the US corn crop is used as feed for meat production. That means that 55% of the water we’ve attributed to corn production gets counted again when we tabulate up numbers for beef, chicken, or other meats.

COUNTERPOINT AND RESPONSE: Prof. Hoekstra agrees with me that water footprints cannot be added in the way I attempted.  Opinions may differ, I suppose, on whether this property is a feature or a bug. But in my view, since mixing a gallon of water with a gallon of water results in two gallons of water it would be nice if water footprints had the same property.

I was very curious to hear a proponent of water footrprint analysis point out flaws in my reasoning or defend waterfootprint.org’s use of these numbers. To that end, I contacted Professor A. Y. Hoekstra, whom I believe to be the primary exponent of water footprint analysis, and shared with him my three concerns.  Graciously, he has responded, and I have included his rebuttals (and my response to them) inline with my arguments above.

In Defense of Food and creationism

On a recent flight I was finally able to digest (ha!) Michael Pollan’s In Defense of Food.  The first part of the book is a historical narrative of the science, policy, and politics of nutritionism in the US.  In Part I, Pollan mounts a devastating critique of US nutritional science and policy. The climax is Chapter 5, “The Melting of the Lipid Hypothesis”, which is perhaps the most important bit of science writing I’ve read all year.    I was left wondering why anyone ever listens to nutritionists.  The only (and minor) weak point in Part I is the tendency to make the nutritionists’ blunders and the grain industry’s lobbying seem more like a nefarious, well-coordinated conspiracy.

But in the Part III of the book, now that Pollan has knocked the scientific wisdom of the day off its altar, it’s time for him to offer an alternative.  And what he proposes isn’t too convincing.  One problem is that Pollan spends so little effort convincing us that there is any sound scientific basis to his recommendations.  In Part I of the book, Pollan adeptly compares case-control studies, cohort studies, and intervention trials…but the entire scientific basis for Pollan’s recommendations on how to eat in Part III appears to be this passage (note the classic correlation-is-not-causation mistake):

People eating a Western diet are prone to a complex of chronic diseases that seldom strike people eating more traditional diets.  Scientists can argue all they want about the biological mechanisms behind this phenomenon, but whichever it is, the solution to the problem would appear to remain very much the same: Stop eating a Western diet.

Instead of science, Pollan’s recommendations rest on cultural traditions.  “Don’t eat anything your grandmother wouldn’t recognize as food,” he says on pg. 148.  “Cultures have had a great deal to say about what and how and why and when and how much we should eat,” says pg. 133.

This train of thought sounds like some creationists’: Both Pollan and creationists poke holes in the scientific orthodoxy and would have us insert tradition in its place. Similarly, creationists think that atheists plot to discredit their work; Pollan warns us to resist the pernicious myths propagated by the “Nutritionalist Industrial Complex”.

The analogy between creationists and In Defense of Food only goes so far, of course.  Most importantly, creationists are not nearly as persuasive in their efforts to poke holes in the scientific orthodoxy. And, even if creationists are wrong, Pollan might still be right. Personally, as weak as I find In Defense of Food’s scientific basis, I think Pollan might be on to something – and I can’t say the same for creationists.

A billion years of sulfidic oceans

In last week’s PNAS, A.H. Knoll and colleagues lay out the controlling feedbacks that they think buffered the Earth’s atmosphere at a low-oxygen state for about a billion years. Very interesting reading for anyone into paleoclimatology, paleooceanography, and/or biogeochemistry in general.

Fact of the day

Over 15,000 cubic kilometers of rain fall on North America each year. (That’s about 0.5 Sverdrups if you like obscure units.)

That flux is equivalent to dumping out a cube of water 700 m on a side every second onto the surface of North America.

More footprints than feet.

Interest in water and water use is growing. Popular magazines have fortold the depletion of the Ogallala Aquifer. Entrepreneurs and venture capitalist-types are looking to water use for business and investment opportunities. How can we measure the impact of new water-efficient processes and technologies — how can we find out if new ideas will work? We can’t…unless, of course, we measure how water is currently used how usage patterns will change in respond to technological or social changes.

Lucikly, researchers are on the job! Waterfootprint.org is one group developing metrics to measure human water use. I found out about them when a friend told me that a single sheet of A4 paper requires 10 liters of water to produce. Ten liters!…for a single sheet! I was incredulous. So I checked out their site, and there it was. “[One sheet of] A4 has a green water footprint of 10 litres.”

But what does it mean that a sheet of paper has a “water footprint” of ten liters? The sad part is that after spending several hours perusing this group’s web site, I suspect the answer is “not much”. I see several problems with the “water footprint” methodology, as I currently understand it.

1. Lack of additivity.

    From the site’s homepage: The water footprint of an individual, community or business is defined as the total volume of freshwater that is used to produce the goods and services consumed by the individual or community or produced by the business.

    As I understand it, if I opened an apple store, sold one apple to my first customer, and closed up shop, my store would have a water footprint of 70 L. But the apple buyer would apparently also has a water footprint 70 L, using the site’s definition. Maybe I am just naive, but I would think that to figure the total water footprint of a nation, we could just add water footprints for all the producers and consumers comprising that nation. Water footprints apparently do not work that way. They are not additive; if we added them, the total water consumption stemming (ha!) from apple related commerce would appear to be 140 L, two times too high.

    2. Attribution error and/or failure to consider substitution effects

      If you dig in deeper to the methods behind calculating “virtual water footprints” or vWFs, it turns out that the total evapotranspiration of water through crops and trees counts as water use. For example the figure for A4 sheets of paper begins with a “production” forest with an evapotranspiration of 600 mm/yr (equivalent to 6000 m3/ha/yr). I can’t wrap my head around this. First of all, if fresh water is a valuable resource, and trees require fresh water for evapotranspiration to live, it seems inevitable that getting rid of trees by cutting them down would save water.  If we cut down a hectare of forest, that’s 6000 m3 of fresh water “saved” a year!  But to the contrary, the water footprint methodology would have us believe that cutting down trees uses water.  Another way to look at the problem is to suppose that the paper company folds up shop, and lets its “production” forest revert back to natural growth.  Does the evapotranspiration of the forest change?  It shouldn’t, at least not by much.  Yet our water footprint has plummeted.

      I have trouble understanding how these characteristics of the “water footprint” are features which render the metric valuable as a policy-making tool.  Instead, I think these characteristics are bugs.  I would personally favor a metric based more on perturbations to the pre-industrial water cycle, for example, on the differences in evapotranspiration between a production forest and an old-growth forest, or between a cornfield and natural grasslands.  But what do the defenders of water footprint analysis say?  These are just my initial thoughts on the approach of water footprint analysis.  I’m sure there is a lot more to say on the subject.